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Making a batch

Filling

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The step where a good batch becomes a set of products, and where contamination is introduced if it is going to be.

Fill by weight

The label declares a net quantity, and for a liquid that is usually a volume, which you deliver most reliably by weighing, because a scale is more accurate than a sight line and does not care about foam.

Establish the target fill weight by filling and weighing several bottles, then hold it.

Check periodically through a run rather than at the start, because a gravity filler slows as the reservoir empties.

Headspace

Enough that the product can expand with temperature without stressing the closure, and that a trigger dip tube has somewhere to sit.

Too little and a warm delivery van produces leaking closures.

Too much and the bottle looks under-filled, which customers notice, and there is more air in contact with the product.

Keeping it clean

This is the contamination step, and a preservative can only cope with so much.

Sanitize the filling equipment, the tubing and any reservoir before a run, and do not leave product standing in tubing between runs.

New bottles are not sterile. For a product with any microbial sensitivity, it is worth knowing how yours are stored and shipped.

And keep the filling area separate from where raw materials are handled.

Capping

To a consistent torque. Under-tightened leaks; over-tightened strips the thread or distorts the liner so it leaks anyway.

A torque gauge is cheap and it removes a common cause of a leaking parcel.

Check the closure is the right one for the formula, which is a compliance question where a child-resistant closure is required.

And inspect along the finished row: fill level, cap seating, label position, anything on the outside of the bottle.

References

No published source. This page is written from practice rather than from published guidance. No extension service or agency publishes on this question for cleaning, so nothing here is cited, and it should be weighed as experience and not as a standard.
Written from the federal regulation and agency guidance named on each page, not from a laboratory or a legal practice. Whether a particular product and a particular label make a cleaner or a pesticide is a determination about your product, and this is not that determination.